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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ), 'gf_id' => 'ORTHO05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ), 'data_identifier' => 'ORTHO05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '445', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p18430' => 'bna', 'A04p20530' => 'bna', 'A07p17960' => 'bna', 'A10p18930' => 'bna', 'A10p18940' => 'bna', 'A10p19040' => 'bna', 'Aa31LG1G13630' => 'aar', 'Aa31LG5G4600' => 'aar', 'Aa31LG5G8420' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.4598' => 'aag', 'Actinidia09309' => 'ach', 'Actinidia23595' => 'ach', 'Ah.01g014670' => 'amhyb', 'Ah.01g014680' => 'amhyb', 'AL4G20580' => 'aly', 'AL4G28460' => 'aly', 'AL6G32580' => 'aly', 'AL6G32770' => 'aly', 'Aqoxy2G00041' => 'aox', 'Aqoxy2G00043' => 'aox', 'Aqoxy3G04272' => 'aox', 'Aqoxy3G04294' => 'aox', 'Aqoxy5G00094' => 'aox', 'Aqoxy7G00471' => 'aox', 'arahy.Tifrunner.gnm1.ann1.06ULD3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.60DDY8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B15C0D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D4P2JU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FWIM6U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SJ3RYI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8N63F' => 'arhy', 'AT2G27040' => 'ath', 'AT2G32940' => 'ath', 'AT5G21030' => 'ath', 'AT5G21150' => 'ath', 'ATR0684G156' => 'atr', 'ATR0684G158' => 'atr', 'ATR0684G187' => 'atr', 'Atru.chr3.2883' => 'acertr', 'Atru.chr6.3266' => 'acertr', 'AUR62015121' => 'cqu', 'AUR62017582' => 'cqu', 'AUR62018462' => 'cqu', 'AUR62018466' => 'cqu', 'AUR62018467' => 'cqu', 'AUR62020956' => 'cqu', 'AUR62020957' => 'cqu', 'AUR62020961' => 'cqu', 'AUR62037160' => 'cqu', 'BcaB01g03948' => 'bca', 'BcaB01g03949' => 'bca', 'BcaB02g10065' => 'bca', 'BcaB05g22769' => 'bca', 'BcaB06g25748' => 'bca', 'BcaB08g36476' => 'bca', 'BcaB08g36478' => 'bca', 'BcaC01g05874' => 'bca', 'BcaC02g10853' => 'bca', 'BcaC03g13836' => 'bca', 'BcaC04g19498' => 'bca', 'BcaC04g19521' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01070' => 'bna', 'BolC2t07102H' => 'bol', 'BolC4t23947H' => 'bol', 'BolC4t27157H' => 'bol', 'BolC9t58352H' => 'bol', 'BolC9t58353H' => 'bol', 'BolC9t58355H' => 'bol', 'BolC9t58368H' => 'bol', 'BolSC94t61271H' => 'bol', 'BolSC94t61275H' => 'bol', 'BraA02t05621Z' => 'bra', 'BraA03t11106Z' => 'bra', 'BraA04t17629Z' => 'bra', 'BraA07t29514Z' => 'bra', 'BraA10t43970Z' => 'bra', 'BraA10t43971Z' => 'bra', 'BraA10t43982Z' => 'bra', 'C03p21540' => 'bna', 'C04p24480' => 'bna', 'C04p56300' => 'bna', 'C09p54910' => 'bna', 'C09p54920' => 'bna', 'C09p55050' => 'bna', 'C09p56650' => 'bna', 'CAN.G134.39' => 'can', 'CAN.G290.21' => 'can', 'CAN.G472.59' => 'can', 'CAN.G65.192' => 'can', 'CAN.G714.11' => 'can', 'CANSAT54G2498' => 'cansat', 'CANSAT78G1712' => 'cansat', 'CARHR119340' => 'chi', 'CARHR126000' => 'chi', 'CARHR126010' => 'chi', 'CARHR126870' => 'chi', 'CARHR191720' => 'chi', 'Carub.0004s0753' => 'cru', 'Carub.0004s1437' => 'cru', 'Carub.0006s1933' => 'cru', 'Carub.0006s1946' => 'cru', 'Ca_06159_v3' => 'car', 'Ca_16219_v3' => 'car', 'Ca_16368_v3' => 'car', 'Cc00_g14230' => 'ccan', 'Cc01_g06780' => 'ccan', 'Cc04_g10830' => 'ccan', 'Cc05_g02730' => 'ccan', 'CDE05G3280' => 'cde', 'CDE06G2053' => 'cde', 'CDE11G1164' => 'cde', 'Cfa010266' => 'cfa', 'Cfa014311' => 'cfa', 'Ciclev10003555m.g' => 'ccl', 'Ciclev10003971m.g' => 'ccl', 'Ciclev10013619m.g' => 'ccl', 'Ciclev10014186m.g' => 'ccl', 'Ciclev10014201m.g' => 'ccl', 'CiPaw.04G109500' => 'cil', 'CiPaw.13G121000' => 'cil', 'CiPaw.14G090600' => 'cil', 'ClCG02G024220' => 'cla', 'ClCG09G011170' => 'cla', 'COL.COLO4_04557' => 'col', 'COL.COLO4_17198' => 'col', 'COL.COLO4_18352' => 'col', 'COL.COLO4_18355' => 'col', 'Cpa.g.sc26.59' => 'cpa', 'Cpa.g.sc600.1' => 'cpa', 'CsaV3_4G017350' => 'csa', 'CsaV3_6G037800' => 'csa', 'CSS0000297' => 'camsi', 'CSS0011124' => 'camsi', 'CSS0028151' => 'camsi', 'CSS0039674' => 'camsi', 'CSS0040352' => 'camsi', 'DCAR_008806' => 'dca', 'DCAR_008808' => 'dca', 'DCAR_018978' => 'dca', 'DCAR_020614' => 'dca', 'DCAR_021136' => 'dca', 'DCAR_021137' => 'dca', 'DCAR_021141' => 'dca', 'DCAR_026519' => 'dca', 'DCAR_026521' => 'dca', 'DCAR_026526' => 'dca', 'Dinv09387' => 'din', 'Dinv10720' => 'din', 'Dinv24001' => 'din', 'Dinv39756' => 'din', 'Duzib011G0001' => 'dzi', 'Duzib011G0002' => 'dzi', 'Duzib058G0001' => 'dzi', 'Duzib133G1066' => 'dzi', 'Duzib168G0889' => 'dzi', 'Duzib168G1053' => 'dzi', 'Duzib168G1724' => 'dzi', 'Duzib170G1140' => 'dzi', 'Duzib172G0001' => 'dzi', 'Duzib249G0001' => 'dzi', 'ECA238G0690' => 'eca', 'ECA238G2669' => 'eca', 'ECA238G3239' => 'eca', 'ECA240G2215' => 'eca', 'ECA240G2558' => 'eca', 'ECA248G1327' => 'eca', 'EL10Ac3g07385' => 'bvu', 'EL10Ac4g08807' => 'bvu', 'EL10Ac9g22361' => 'bvu', 'EL10Ac9g22823' => 'bvu', 'Eucgr.B03780' => 'egr', 'Eucgr.E02365' => 'egr', 'Eucgr.J00634' => 'egr', 'Eucgr.K00735' => 'egr', 'Eucgr.K00736' => 'egr', 'Eucgr.L03052' => 'egr', 'Eucgr.L03643' => 'egr', 'FAN01G0285' => 'fan', 'FAN01G2083' => 'fan', 'FAN02G4428' => 'fan', 'FAN05G4160' => 'fan', 'FAN06G4540' => 'fan', 'FAN07G1225' => 'fan', 'FAN07G1847' => 'fan', 'FAN07G2418' => 'fan', 'FAN09G2151' => 'fan', 'FAN10G0449' => 'fan', 'FAN11G2923' => 'fan', 'FAN12G2656' => 'fan', 'FAN12G3294' => 'fan', 'FAN12G3766' => 'fan', 'FAN14G3283' => 'fan', 'FAN16G3417' => 'fan', 'FAN22G0596' => 'fan', 'FAN22G2209' => 'fan', 'FAN25G0909' => 'fan', 'FAN25G2028' => 'fan', 'FvH4_3g27260' => 'fve', 'FvH4_4g08040' => 'fve', 'FvH4_4g08050' => 'fve', 'FvH4_4g13080' => 'fve', 'FvH4_6g42040' => 'fve', 'FvH4_7g04840' => 'fve', 'Glyma.02G274900' => 'gma', 'Glyma.06G314500' => 'gma', 'Glyma.13G193200' => 'gma', 'Glyma.14G041100' => 'gma', 'Glyma.20G052500' => 'gma', 'Gohir.A05G101800' => 'ghi', 'Gohir.A07G168500' => 'ghi', 'Gohir.A08G196800' => 'ghi', 'Gohir.D05G101500' => 'ghi', 'Gohir.D07G175000' => 'ghi', 'Gohir.D08G214000' => 'ghi', 'Gorai.001G195700' => 'gra', 'Gorai.004G228100' => 'gra', 'Gorai.009G105600' => 'gra', 'GSVIVG01001941001' => 'vvi', 'GSVIVG01025868001' => 'vvi', 'GSVIVG01030512001' => 'vvi', 'GSVIVG01037488001' => 'vvi', 'HanXRQChr03g0091711' => 'han', 'HanXRQChr14g0445731' => 'han', 'HanXRQChr14g0446971' => 'han', 'HanXRQChr14g0446981' => 'han', 'HanXRQChr14g0447001' => 'han', 'HanXRQChr14g0447541' => 'han', 'HanXRQChr14g0459081' => 'han', 'Haze_12760' => 'cav', 'Haze_23676' => 'cav', 'Hma1.2p1_0121F.1_g057470' => 'hma', 'Hma1.2p1_0218F.1_g092800' => 'hma', 'Hma1.2p1_0765F.1_g215080' => 'hma', 'HPP92_000158' => 'vpl', 'HPP92_000195' => 'vpl', 'HPP92_000218' => 'vpl', 'HPP92_000241' => 'vpl', 'HPP92_006665' => 'vpl', 'Hund01351' => 'sun', 'Hund03708' => 'sun', 'Hund08088' => 'sun', 'Lalb_Chr04g0249631' => 'lal', 'Lalb_Chr15g0080261' => 'lal', 'Lalb_Chr17g0347571' => 'lal', 'Lalb_Chr18g0049121' => 'lal', 'Lalb_Chr22g0360871' => 'lal', 'Lj1C248T1' => 'lonja', 'Lj1C272T5' => 'lonja', 'Lj1C783T8' => 'lonja', 'Lj2C935T1' => 'lonja', 'Lj3g0019777' => 'lja', 'Lj5g0003224' => 'lja', 'Lj5g0007702' => 'lja', 'Lj5g0011195' => 'lja', 'Lj6g0000620' => 'lja', 'Lj6g0013334' => 'lja', 'Lj9C704G17' => 'lonja', 'LjContig00564g0023857' => 'lja', 'Lsat_1_v5_gn_2_63381' => 'lsa', 'Lsat_1_v5_gn_2_63400' => 'lsa', 'Lsat_1_v5_gn_2_63421' => 'lsa', 'Lsat_1_v5_gn_3_115620' => 'lsa', 'Lsat_1_v5_gn_3_116161' => 'lsa', 'Lsat_1_v5_gn_9_106140' => 'lsa', 'Lsat_1_v5_gn_9_83041' => 'lsa', 'Manes.02G209900' => 'mes', 'Manes.13G066164' => 'mes', 'Manes.18G121900' => 'mes', 'Mapoly0045s0024' => 'mpo', 'Mapoly0063s0058' => 'mpo', 'Mapoly0065s0059' => 'mpo', 'MBI01_g23471_MAGBIO' => 'mbi', 'MBI06_g18014_MAGBIO' => 'mbi', 'MBI08_g30371_MAGBIO' => 'mbi', 'MBI13_g00565_MAGBIO' => 'mbi', 'MBI18_g14090_MAGBIO' => 'mbi', 'MBI19_g03676_MAGBIO' => 'mbi', 'MD03G1164000' => 'mdo', 'MD07G1052200' => 'mdo', 'MD07G1052400' => 'mdo', 'MD09G1115300' => 'mdo', 'MD11G1182100' => 'mdo', 'Medtr3g010650' => 'mtr', 'Medtr3g078647' => 'mtr', 'Medtr3g083300' => 'mtr', 'Medtr5g087870' => 'mtr', 'Medtr5g087890' => 'mtr', 'Medtr6g043180' => 'mtr', 'Medtr7g107230' => 'mtr', 'MELO3C014440.2' => 'cme', 'MELO3C014706.2' => 'cme', 'Migut.D00694' => 'egut', 'Migut.M00131' => 'egut', 'Migut.M00133' => 'egut', 'Migut.N01871' => 'egut', 'Migut.O00200' => 'egut', 'MSTRG.14863' => 'ama', 'Nitab4.5_0000130g0120' => 'nta', 'Nitab4.5_0000428g0010' => 'nta', 'Nitab4.5_0000510g0050' => 'nta', 'Nitab4.5_0001812g0120' => 'nta', 'Nitab4.5_0002368g0130' => 'nta', 'Nitab4.5_0002687g0040' => 'nta', 'Nitab4.5_0002915g0040' => 'nta', 'Nitab4.5_0004903g0020' => 'nta', 'Nitab4.5_0009321g0010' => 'nta', 'Nitab4.5_0010831g0030' => 'nta', 'Nn1g07314' => 'nnu', 'Nn7g37235' => 'nnu', 'Oeu008546.1' => 'oeu', 'Oeu040183.1' => 'oeu', 'Oeu048079.2' => 'oeu', 'Oeu063620.1' => 'oeu', 'Os01g0275200' => 'osa', 'Os01g0275600' => 'osa', 'Os04g0151800' => 'osa', 'Os07g0265600' => 'osa', 'Peaxi162Scf00050g00169' => 'pax', 'Peaxi162Scf00089g01025' => 'pax', 'Peaxi162Scf00220g00110' => 'pax', 'Peaxi162Scf00520g00076' => 'pax', 'Peaxi162Scf00973g00316' => 'pax', 'Peaxi162Scf01333g00148' => 'pax', 'PGR102G0604' => 'pgr', 'PGR119G0559' => 'pgr', 'PGR142G1328' => 'pgr', 'PGSC0003DMG400022707' => 'stu', 'PGSC0003DMG400027002' => 'stu', 'PGSC0003DMG400027529' => 'stu', 'Phvul.006G021200' => 'pvu', 'Phvul.008G206500' => 'pvu', 'Phvul.008G206600' => 'pvu', 'Phvul.011G169400' => 'pvu', 'Potri.001G219700' => 'ptr', 'Potri.006G025900' => 'ptr', 'Potri.008G010500' => 'ptr', 'Potri.014G159400' => 'ptr', 'Potri.016G024200' => 'ptr', 'Prupe.2G056600' => 'ppe', 'Prupe.2G056700' => 'ppe', 'Prupe.3G209300' => 'ppe', 'Prupe.6G154800' => 'ppe', 'Psat2g022680' => 'psa', 'Psat5g101240' => 'psa', 'Psat5g110040' => 'psa', 'PSO339G0407' => 'pso', 'PSO541G1998' => 'pso', 'PSO541G2228' => 'pso', 'PSO675G0039' => 'pso', 'PSO675G0189' => 'pso', 'PSO675G4457' => 'pso', 'QL01p020174' => 'qlo', 'QL04p051677' => 'qlo', 'QL08p030409' => 'qlo', 'QL93p1871_0004' => 'qlo', 'RcHm_v2.0_Chr1g0322921' => 'rch', 'RcHm_v2.0_Chr1g0330301' => 'rch', 'RcHm_v2.0_Chr2g0157951' => 'rch', 'RcHm_v2.0_Chr2g0157971' => 'rch', 'RcHm_v2.0_Chr2g0157981' => 'rch', 'RcHm_v2.0_Chr4g0412801' => 'rch', 'RcHm_v2.0_Chr5g0049901' => 'rch', 'RcHm_v2.0_Chr7g0206231' => 'rch', 'Rhsim01G0195100' => 'rsi', 'Rhsim01G0196200' => 'rsi', 'Rhsim01G0196300' => 'rsi', 'Rhsim06G0168000' => 'rsi', 'Sabra06G0019100' => 'sbr', 'Sabra08G0006300' => 'sbr', 'Sabra14G0121100' => 'sbr', 'Sabra16G0030100' => 'sbr', 'Sabra16G0124600' => 'sbr', 'SalBow1G3629' => 'sbo', 'SalBow5G1497' => 'sbo', 'SalBow6G2542' => 'sbo', 'SalBow6G6989' => 'sbo', 'SalBow7G2286' => 'sbo', 'Sc15g0007310' => 'sci', 'Sc20g0001020' => 'sci', 'Sc21g0001120' => 'sci', 'Sed0016540' => 'sed', 'Sed0025198' => 'sed', 'Sed0025525' => 'sed', 'Sed0026403' => 'sed', 'Sed0026464' => 'sed', 'SEGI_36421' => 'sgi', 'SEGI_39827' => 'sgi', 'SGA_v2.0_scaffold196G41002' => 'sas', 'SGA_v2.0_scaffold26G11366' => 'sas', 'SGA_v2.0_scaffold29G12168' => 'sas', 'SGA_v2.0_scaffold34G13788' => 'sas', 'SGA_v2.0_scaffold79G25565' => 'sas', 'SGA_v2.0_scaffold90G27791' => 'sas', 'SHI10067' => 'shi', 'SHI25347' => 'shi', 'SMO146G0154' => 'smo', 'Solyc01g008960.3' => 'sly', 'Solyc01g096750.1' => 'sly', 'Solyc03g111760.3' => 'sly', 'Solyc06g073530.3' => 'sly', 'Solyc06g073540.4' => 'sly', 'Solyc07g049500.3' => 'sly', 'Sopen01g004450' => 'spe', 'Sopen01g040460' => 'spe', 'Sopen03g030870' => 'spe', 'Sopen06g029890' => 'spe', 'Sopen06g029900' => 'spe', 'Sopen07g024850' => 'spe', 'Sp4g08240' => 'spa', 'Sp4g15300' => 'spa', 'Sp6g23370' => 'spa', 'Sp6g23510' => 'spa', 'TAR627G0232' => 'tar', 'TAR633G1821' => 'tar', 'TAR636G0402' => 'tar', 'THA.LOC104799583' => 'tha', 'THA.LOC104800485' => 'tha', 'THA.LOC104826132' => 'tha', 'Thecc.01G183100' => 'tca', 'Thecc.09G338500' => 'tca', 'Thhalv10001902m.g' => 'esa', 'Thhalv10012624m.g' => 'esa', 'Thhalv10015501m.g' => 'esa', 'Thhalv10016224m.g' => 'esa', 'TPR.G19332' => 'tpr', 'TPR.G22223' => 'tpr', 'TPR.G24744' => 'tpr', 'TPR.G27312' => 'tpr', 'TPR.G5145' => 'tpr', 'TWI31G0029' => 'twi', 'TWI36G0885' => 'twi', 'TWI73G1215' => 'twi', 'TWI79G0571' => 'twi', 'unitig_22.g6185' => 'ugi', 'vmacro10817' => 'vma', 'vmacro12157' => 'vma', 'vmacro14287' => 'vma', 'vmacro20777' => 'vma', 'VMungo0540G1957' => 'vmu', 'VMungo1127G1671' => 'vmu', 'VMungo1215G3369' => 'vmu', 'Zm00001eb128780' => 'zma', 'Zm00001eb297760' => 'zma', 'Zm00001eb308470' => 'zma', 'Zm00001eb332830' => 'zma' ) $gf_id = 'ORTHO05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001258' ) $data_identifier = 'ORTHO05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 6, 'arhy' => (int) 7, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 9, 'bca' => (int) 12, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 10, 'din' => (int) 4, 'dzi' => (int) 10, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 7, 'fan' => (int) 20, 'fve' => (int) 6, 'gma' => (int) 5, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 5, 'lja' => (int) 7, 'lsa' => (int) 7, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mdo' => (int) 5, 'mtr' => (int) 7, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 3, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb332830' $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